Variant report

Variant	rs12613652
Chromosome Location	chr2:49082000-49082001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49080769..49083086-chr2:49086686..49089047,2	MCF-7	breast:
2	chr2:49081319..49083197-chr2:49107259..49109037,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13001105	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13002543	0.91[ASN][1000 genomes]
rs13002594	0.94[ASN][1000 genomes]
rs13019604	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13027348	0.94[ASN][1000 genomes]
rs13030500	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13030632	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030729	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13034735	0.94[ASN][1000 genomes]
rs17483876	0.86[AFR][1000 genomes]
rs34075428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34965941	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35451419	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36080348	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934824	0.94[ASN][1000 genomes]
rs3934825	0.94[ASN][1000 genomes]
rs3934826	0.94[ASN][1000 genomes]
rs3934827	0.94[ASN][1000 genomes]
rs4331561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4432506	0.82[AFR][1000 genomes]
rs56218371	0.84[AFR][1000 genomes]
rs57463767	0.87[AFR][1000 genomes]
rs57694457	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58176203	0.93[AFR][1000 genomes]
rs59230684	0.87[AFR][1000 genomes]
rs66481918	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72811832	0.81[AFR][1000 genomes]
rs72811860	0.83[AFR][1000 genomes]
rs72823283	0.89[AFR][1000 genomes]
rs7567401	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv998864	chr2:49015878-49230000	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:49076000-49082800	Enhancers	HMEC	breast
2	chr2:49076400-49084800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:49079400-49082200	Weak transcription	NHEK	skin
4	chr2:49079600-49082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:49080200-49082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:49080200-49083200	Enhancers	Stomach Smooth Muscle	stomach
7	chr2:49080400-49082200	Enhancers	HSMMtube	muscle
8	chr2:49080800-49082000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:49081400-49082200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:49081400-49082200	Weak transcription	NHLF	lung
11	chr2:49081400-49082400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:49081800-49082600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:49081800-49085800	Enhancers	Ovary	ovary
14	chr2:49082000-49082200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links